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Roy C, He X, Gahtyari NC, Mahapatra S, Singh PK. Managing spot blotch disease in wheat: Conventional to molecular aspects. FRONTIERS IN PLANT SCIENCE 2023; 14:1098648. [PMID: 36895883 PMCID: PMC9990093 DOI: 10.3389/fpls.2023.1098648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Spot blotch (SB) caused by Bipolaris sorokiniana (teleomorph Cochliobolus sativus) is one of the devastating diseases of wheat in the warm and humid growing areas around the world. B. sorokiniana can infect leaves, stem, roots, rachis and seeds, and is able to produce toxins like helminthosporol and sorokinianin. No wheat variety is immune to SB; hence, an integrated disease management strategy is indispensable in disease prone areas. A range of fungicides, especially the triazole group, have shown good effects in reducing the disease, and crop-rotation, tillage and early sowing are among the favorable cultural management methods. Resistance is mostly quantitative, being governed by QTLs with minor effects, mapped on all the wheat chromosomes. Only four QTLs with major effects have been designated as Sb1 through Sb4. Despite, marker assisted breeding for SB resistance in wheat is scarce. Better understanding of wheat genome assemblies, functional genomics and cloning of resistance genes will further accelerate breeding for SB resistance in wheat.
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Affiliation(s)
- Chandan Roy
- Department of Genetics and Plant Breeding, Agriculture University, Jodhpur, Rajasthan, India
| | - Xinyao He
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Mexico DF, Mexico
| | - Navin C. Gahtyari
- Crop Improvement Division, ICAR–Vivekanand Parvatiya Krishi Anushandhan Sansthan, Almora, Uttarakhand, India
| | - Sunita Mahapatra
- Department of Plant Pathology, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, India
| | - Pawan K. Singh
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Mexico DF, Mexico
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Kumar S, Pradhan AK, Kumar U, Dhillon GS, Kaur S, Budhlakoti N, Mishra DC, Singh AK, Singh R, Kumari J, Kumaran VV, Mishra VK, Bhati PK, Das S, Chand R, Singh K, Kumar S. Validation of Novel spot blotch disease resistance alleles identified in unexplored wheat (Triticum aestivum L.) germplasm lines through KASP markers. BMC PLANT BIOLOGY 2022; 22:618. [PMID: 36577935 PMCID: PMC9798658 DOI: 10.1186/s12870-022-04013-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND During the last few decades, the diverse sources of resistance, several genes and QTLs for spot blotch resistance have been identified. However, a large set of germplasm lines are still unexplored that have the potential to develop highly resistant wheat cultivars for the target environments. Therefore, the identification of new sources of resistance to spot blotch is essential for breeding programmes to develop spot blotch resistant cultivars and sustain wheat production. The association mapping panel of 294 diverse bread wheat accessions was used to explore new sources of spot blotch disease resistance and to identify genomic regions using genome wide association analysis (GWAS). The genotypes were tested in replicated trials for spot blotch disease at three major hot spots in India (Varanasi in UP, Pusa in Bihar, and Cooch Behar in West Bengal). The area under the disease progress curve (AUDPC) was calculated to assess the level of resistance in each genotype. RESULTS A total of 19 highly and 76 moderately resistant lines were identified. Three accessions (EC664204, IC534306 and IC535188) were nearly immune to spot blotch disease. The genotyping of all accessions resulted in a total of 16,787 high-quality polymorphic SNPs. The GWAS was performed using a Compressed Mixed Linear Model (CMLM) and a Mixed Linear Model (MLM). A total of seven significant MTAs, common in both the models and consistent across the environment, were further validated to develop KASP markers. Four MTAs (AX-94710084, AX-94865722, AX-95135556, and AX-94529408) on three chromosomes (2AL, 2BL, and 3BL) have been successfully validated through the KASP marker. CONCLUSIONS The new source of resistance was identified from unexplored germplasm lines. The genomic regions identified through GWAS were validated through KASP markers. The marker information and the highly resistant sources are valuable resources to rapidly develop immune or near immune wheat varieties.
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Affiliation(s)
- Suneel Kumar
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | - Uttam Kumar
- Borlaug Institute for South Asia, NASC Complex, DPS Marg, New Delhi, India.
| | | | - Satinder Kaur
- Punjab Agricultural University, Ludhiana, Punjab, India
| | - Neeraj Budhlakoti
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rakesh Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Jyoti Kumari
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Vikas V Kumaran
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, India
| | | | | | - Saikat Das
- Uttar Banga Krishi Vishwavidyalaya, Pundibari, Coochbehar, India
| | - Ramesh Chand
- Banaras Hindu University, Uttar Pradesh, Varanasi, India
| | - Kuldeep Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sundeep Kumar
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India.
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Ma QZ, Wu HY, Xie SP, Zhao BS, Yin XM, Ding SL, Guo YS, Xu C, Zang R, Geng YH, Zhang M. BsTup1 is required for growth, conidiogenesis, stress response and pathogenicity of Bipolaris sorokiniana. Int J Biol Macromol 2022; 220:721-732. [PMID: 35981683 DOI: 10.1016/j.ijbiomac.2022.07.250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 11/05/2022]
Abstract
Tup1, a conserved transcriptional repressor, plays a critical role in the growth and development of fungi. Here, we identified a BsTup1 gene from the plant pathogenic fungus Bipolaris sorokiniana. The expression of BsTup1 showed a more than three-fold increase during the conidial stage compared with mycelium stage. Deletion of BsTup1 led to decrease hyphal growth and defect in conidia formation. A significant difference was detected in osmotic, oxidative, or cell wall stress responses between the WT and ΔBsTup1 strains. Pathogenicity assays showed that virulence of the ΔBsTup1 mutant was dramatically decreased on wheat and barely leaves. Moreover, it was observed that hyphal tips of the mutants could not form appressorium-like structures on the inner epidermis of onion and barley coleoptile. Yeast two-hybrid assays indicated that BsTup1 could interact with the BsSsn6. RNAseq revealed significant transcriptional changes in the ΔBsTup1 mutant with 2369 genes down-regulated and 2962 genes up-regulated. In these genes, we found that a subset of genes involved in fungal growth, sporulation, cell wall integrity, osmotic stress, oxidation stress, and pathogenicity, which were misregulated in the ΔBsTup1 mutant. These data revealed that BsTup1 has multiple functions in fungal growth, development, stress response and pathogenesis in B. sorokiniana.
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Affiliation(s)
- Qing-Zhou Ma
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Hai-Yan Wu
- Analytical Instrument Center, Henan Agricultural University, Zhengzhou 450002, China
| | - Shun-Pei Xie
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Bing-Sen Zhao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Xin-Ming Yin
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Sheng-Li Ding
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Ya-Shuang Guo
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Chao Xu
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Rui Zang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Yue-Hua Geng
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China.
| | - Meng Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China.
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Juliana P, He X, Poland J, Roy KK, Malaker PK, Mishra VK, Chand R, Shrestha S, Kumar U, Roy C, Gahtyari NC, Joshi AK, Singh RP, Singh PK. Genomic selection for spot blotch in bread wheat breeding panels, full-sibs and half-sibs and index-based selection for spot blotch, heading and plant height. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1965-1983. [PMID: 35416483 PMCID: PMC9205839 DOI: 10.1007/s00122-022-04087-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
KEY MESSAGE Genomic selection is a promising tool to select for spot blotch resistance and index-based selection can simultaneously select for spot blotch resistance, heading and plant height. A major biotic stress challenging bread wheat production in regions characterized by humid and warm weather is spot blotch caused by the fungus Bipolaris sorokiniana. Since genomic selection (GS) is a promising selection tool, we evaluated its potential for spot blotch in seven breeding panels comprising 6736 advanced lines from the International Maize and Wheat Improvement Center. Our results indicated moderately high mean genomic prediction accuracies of 0.53 and 0.40 within and across breeding panels, respectively which were on average 177.6% and 60.4% higher than the mean accuracies from fixed effects models using selected spot blotch loci. Genomic prediction was also evaluated in full-sibs and half-sibs panels and sibs were predicted with the highest mean accuracy (0.63) from a composite training population with random full-sibs and half-sibs. The mean accuracies when full-sibs were predicted from other full-sibs within families and when full-sibs panels were predicted from other half-sibs panels were 0.47 and 0.44, respectively. Comparison of GS with phenotypic selection (PS) of the top 10% of resistant lines suggested that GS could be an ideal tool to discard susceptible lines, as greater than 90% of the susceptible lines discarded by PS were also discarded by GS. We have also reported the evaluation of selection indices to simultaneously select non-late and non-tall genotypes with low spot blotch phenotypic values and genomic-estimated breeding values. Overall, this study demonstrates the potential of integrating GS and index-based selection for improving spot blotch resistance in bread wheat.
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Affiliation(s)
- Philomin Juliana
- Borlaug Institute for South Asia (BISA), Ludhiana, Punjab, India
| | - Xinyao He
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico
| | - Jesse Poland
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Krishna K Roy
- Bangladesh Wheat and Maize Research Institute, Nashipur, Dinajpur, 5200, Bangladesh
| | - Paritosh K Malaker
- Bangladesh Wheat and Maize Research Institute, Nashipur, Dinajpur, 5200, Bangladesh
| | - Vinod K Mishra
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Ramesh Chand
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Sandesh Shrestha
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA
| | - Uttam Kumar
- Borlaug Institute for South Asia (BISA), Ludhiana, Punjab, India
| | - Chandan Roy
- Department of Plant Breeding and Genetics, Bihar Agricultural University, Sabour, Bihar, 813210, India
| | - Navin C Gahtyari
- ICAR-Vivekanand Parvatiya Krishi Anushandhan Sansthan, Almora, Uttarakhand, 263601, India
| | - Arun K Joshi
- Borlaug Institute for South Asia (BISA), Ludhiana, Punjab, India
- CIMMYT-India, NASC Complex, DPS Marg, New Delhi, India
| | - Ravi P Singh
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico.
| | - Pawan K Singh
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico, DF, Mexico.
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Juliana P, He X, Poland J, Shrestha S, Joshi AK, Huerta-Espino J, Govindan V, Crespo-Herrera LA, Mondal S, Kumar U, Bhati PK, Vishwakarma M, Singh RP, Singh PK. Genome-Wide Association Mapping Indicates Quantitative Genetic Control of Spot Blotch Resistance in Bread Wheat and the Favorable Effects of Some Spot Blotch Loci on Grain Yield. FRONTIERS IN PLANT SCIENCE 2022; 13:835095. [PMID: 35310648 PMCID: PMC8928540 DOI: 10.3389/fpls.2022.835095] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Spot blotch caused by the fungus Bipolaris sorokiniana poses a serious threat to bread wheat production in warm and humid wheat-growing regions of the world. Hence, the major objective of this study was to identify consistent genotyping-by-sequencing (GBS) markers associated with spot blotch resistance using genome-wide association mapping on a large set of 6,736 advanced bread wheat breeding lines from the International Maize and Wheat Improvement Center. These lines were phenotyped as seven panels at Agua Fria, Mexico between the 2013-2014 and 2019-2020 crop cycles. We identified 214 significant spot blotch associated GBS markers in all the panels, among which only 96 were significant in more than one panel, indicating a strong environmental effect on the trait and highlights the need for multiple phenotypic evaluations to identify lines with stable spot blotch resistance. The 96 consistent GBS markers were on chromosomes 1A, 1B, 1D, 2A, 3B, 4A, 5B, 5D, 6B, 7A, 7B, and 7D, including markers possibly linked to the Lr46, Sb1, Sb2 and Sb3 genes. We also report the association of the 2NS translocation from Aegilops ventricosa with spot blotch resistance in some environments. Moreover, the spot blotch favorable alleles at the 2NS translocation and two markers on chromosome 3BS (3B_2280114 and 3B_5601689) were associated with increased grain yield evaluated at several environments in Mexico and India, implying that selection for favorable alleles at these loci could enable simultaneous improvement for high grain yield and spot blotch resistance. Furthermore, a significant relationship between the percentage of favorable alleles in the lines and their spot blotch response was observed, which taken together with the multiple minor effect loci identified to be associated with spot blotch in this study, indicate quantitative genetic control of resistance. Overall, the results presented here have extended our knowledge on the genetic basis of spot blotch resistance in bread wheat and further efforts to improve genetic resistance to the disease are needed for reducing current and future losses under climate change.
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Affiliation(s)
| | - Xinyao He
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Jesse Poland
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, United States
| | - Sandesh Shrestha
- Department of Plant Pathology, Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, United States
| | - Arun K. Joshi
- Borlaug Institute for South Asia (BISA), Ludhiana, India
- International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India
| | - Julio Huerta-Espino
- Campo Experimental Valle de Mexico, Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias (INIFAP), Chapingo, Mexico
| | - Velu Govindan
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | - Suchismita Mondal
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Uttam Kumar
- Borlaug Institute for South Asia (BISA), Ludhiana, India
| | - Pradeep K. Bhati
- International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India
| | - Manish Vishwakarma
- International Maize and Wheat Improvement Center (CIMMYT), New Delhi, India
| | - Ravi P. Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Pawan K. Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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6
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Biology and Management of Spot Blotch Pathogen Bipolaris sorokiniana of Wheat. Fungal Biol 2022. [DOI: 10.1007/978-981-16-8877-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Tomar V, Singh D, Dhillon GS, Singh RP, Poland J, Joshi AK, Singh PK, Bhati PK, Kumar S, Rahman M, Tiwari BS, Kumar U. New QTLs for Spot Blotch Disease Resistance in Wheat ( Triticum aestivum L.) Using Genome-Wide Association Mapping. Front Genet 2021; 11:613217. [PMID: 33519916 PMCID: PMC7841440 DOI: 10.3389/fgene.2020.613217] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/10/2020] [Indexed: 11/13/2022] Open
Abstract
Spot blotch disease caused by Bipolaris sorokiniana is a major constraint for wheat production in tropics and subtropics. The introgression of spot blotch resistance alleles to the disease susceptible lines is critical to securing the wheat production in these regions. Although genome-wide association studies (GWASs) for spot blotch were attempted earlier, the present study focused on identifying new quantitative trait loci (QTLs) for spot blotch under natural disease pressure in diverse field conditions. A total of 139 advanced spring wheat lines were evaluated in three environments (three years and two locations) in India and Bangladesh. The GWAS using 14,063 polymorphic genotyping-by-sequencing (GBS) markers identified eight QTLs associated with spot blotch disease resistance belonging to eight chromosomes across the wheat genome. Here, we report the identified marker–trait associations (MTAs), along with the allele effects associated with the disease. The functional annotation of the significant markers identified NBS-LRR, MADS-box transcription factor, and 34 other plant-related protein families across multiple chromosomal regions. The results indicate four promising new QTLs on chromosomes 1A (497.2 Mb), 1D (89.84 Mb), 2B (421.92 Mb), and 6D (6.84 Mb) associated with several disease resistance protein families. These results provide insights into new genomic regions associated with spot blotch disease, and with additional validation, could be utilized in disease resistance breeding efforts in wheat development.
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Affiliation(s)
- Vipin Tomar
- Borlaug Institute for South Asia, Ludhiana, India.,Institute of Advanced Research, Gandhinagar, Gujarat, India
| | - Daljit Singh
- The Climate Corporation, Bayer Crop Science, Creve Coeur, MO, United States
| | - Guriqbal Singh Dhillon
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, India
| | - Ravi Prakash Singh
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Arun Kumar Joshi
- Borlaug Institute for South Asia, Ludhiana, India.,International Maize and Wheat Improvement Centre, New Delhi, India
| | - Pawan Kumar Singh
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | - Suneel Kumar
- Borlaug Institute for South Asia, Ludhiana, India
| | - Mokhlesur Rahman
- Wheat Research Center, Regional Agricultural Research Station, Bangladesh Agricultural Research Institute, Jamalpur, Bangladesh
| | | | - Uttam Kumar
- Borlaug Institute for South Asia, Ludhiana, India.,Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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Jamil M, Ali A, Gul A, Ghafoor A, Ibrahim AMH, Mujeeb-Kazi A. Genome-Wide Association Studies for Spot Blotch (Cochliobolus sativus) Resistance in Bread Wheat Using Genotyping-by-Sequencing. PHYTOPATHOLOGY 2018; 108:1307-1314. [PMID: 30277843 DOI: 10.1094/phyto-02-18-0047-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Spot blotch is a severe biotic menace of wheat caused by Cochliobolus sativus (syn. Bipolaris sorokiniana). Spot blotch is liable to major yield losses in warm humid regions. A genome-wide association study using genotyping-by-sequencing (GBS) markers was conducted to identify genomic regions associated with spot blotch resistance in a diversity panel of 159 spring wheat genotypes. In total, 87,096 GBS markers covering the whole genome, with an average polymorphism information content value of 0.276, were applied. Linkage disequilibrium (LD) analysis indicated that the LD decay extent was approximately 100 Mbp. The panel was evaluated for disease severity (DS) and area under disease progress curve (AUDPC) for 2 years. In total, 24 marker-trait associations (MTA) were identified for DS and AUDPC of spot blotch, with 11 on chromosome 5B, 3 on 3A, 2 on 6B, and 1 each on 1A, 2A, 1D, 2D, 4B, 5A, 7A, and 7B. A marker on chromosome 7B significantly explained 14% of the phenotypic variation of spot blotch severity as well as 11% of AUDPC. Five markers-three on chromosome 5B, one on 3A, and one on 7B-were associated with both DS and AUDPC with R2 ranging from 8 to 12%. Significant MTA can be utilized to develop wheat germplasm with resistance to spot blotch.
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Affiliation(s)
- Muhammad Jamil
- First and second authors: Department of Botany, University of Sargohda, Sargodha. Pakistan; third author: Atta-ur-Rehman School of Applied Biosciences, National University of Science and Technology, Islamabad, Pakistan and United States Department of Agriculture-Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA; fourth author: Plant Genetic Resources Institute, National Agriculture Research Center, Islamabad, Pakistan; fifth author: Soil and Crop Sciences Department, Texas A&M University, TX 77843-2474; and sixth author: Texas A&M University, Amarillo, TX 79106
| | - Aamir Ali
- First and second authors: Department of Botany, University of Sargohda, Sargodha. Pakistan; third author: Atta-ur-Rehman School of Applied Biosciences, National University of Science and Technology, Islamabad, Pakistan and United States Department of Agriculture-Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA; fourth author: Plant Genetic Resources Institute, National Agriculture Research Center, Islamabad, Pakistan; fifth author: Soil and Crop Sciences Department, Texas A&M University, TX 77843-2474; and sixth author: Texas A&M University, Amarillo, TX 79106
| | - Alvina Gul
- First and second authors: Department of Botany, University of Sargohda, Sargodha. Pakistan; third author: Atta-ur-Rehman School of Applied Biosciences, National University of Science and Technology, Islamabad, Pakistan and United States Department of Agriculture-Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA; fourth author: Plant Genetic Resources Institute, National Agriculture Research Center, Islamabad, Pakistan; fifth author: Soil and Crop Sciences Department, Texas A&M University, TX 77843-2474; and sixth author: Texas A&M University, Amarillo, TX 79106
| | - Abdul Ghafoor
- First and second authors: Department of Botany, University of Sargohda, Sargodha. Pakistan; third author: Atta-ur-Rehman School of Applied Biosciences, National University of Science and Technology, Islamabad, Pakistan and United States Department of Agriculture-Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA; fourth author: Plant Genetic Resources Institute, National Agriculture Research Center, Islamabad, Pakistan; fifth author: Soil and Crop Sciences Department, Texas A&M University, TX 77843-2474; and sixth author: Texas A&M University, Amarillo, TX 79106
| | - Amir M H Ibrahim
- First and second authors: Department of Botany, University of Sargohda, Sargodha. Pakistan; third author: Atta-ur-Rehman School of Applied Biosciences, National University of Science and Technology, Islamabad, Pakistan and United States Department of Agriculture-Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA; fourth author: Plant Genetic Resources Institute, National Agriculture Research Center, Islamabad, Pakistan; fifth author: Soil and Crop Sciences Department, Texas A&M University, TX 77843-2474; and sixth author: Texas A&M University, Amarillo, TX 79106
| | - Abdul Mujeeb-Kazi
- First and second authors: Department of Botany, University of Sargohda, Sargodha. Pakistan; third author: Atta-ur-Rehman School of Applied Biosciences, National University of Science and Technology, Islamabad, Pakistan and United States Department of Agriculture-Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA; fourth author: Plant Genetic Resources Institute, National Agriculture Research Center, Islamabad, Pakistan; fifth author: Soil and Crop Sciences Department, Texas A&M University, TX 77843-2474; and sixth author: Texas A&M University, Amarillo, TX 79106
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9
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Ayana GT, Ali S, Sidhu JS, Gonzalez Hernandez JL, Turnipseed B, Sehgal SK. Genome-Wide Association Study for Spot Blotch Resistance in Hard Winter Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:926. [PMID: 30034404 PMCID: PMC6043670 DOI: 10.3389/fpls.2018.00926] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/11/2018] [Indexed: 05/06/2023]
Abstract
Spot blotch (SB) caused by Cochliobolus sativus (anamorph: Bipolaris sorokiniana) is an economically important disease of wheat worldwide. Under a severe epidemic condition, the disease can cause yield losses up to 70%. Previous approaches like bi-parental mapping for identifying SB resistant genes/QTLs exploited only a limited portion of the available genetic diversity with a lower capacity to detect polygenic traits, and had a lower marker density. In this study, we performed genome-wide association study (GWAS) for SB resistance in hard winter wheat association mapping panel (HWWAMP) of 294 genotypes. The HWWAMP was evaluated for response to B. sorokiniana (isolate SD40), and a range of reactions was observed with 10 resistant, 38 moderately resistant, 120 moderately resistant- moderately susceptible, 111 moderately susceptible, and 15 susceptible genotypes. GWAS using 15,590 high-quality SNPs and 294 genotypes we identified six QTLs (p = <0.001) on chromosomes 2D, 3A, 4A, 4B, 5A, and 7B that collectively explained 30% of the total variation for SB resistance. Highly associated SNPs were identified for all six QTLs, QSb.sdsu-2D.1 (SNP: Kukri_c31121_1460, R2 = 4%), QSb.sdsu-3A.1 (SNP: Excalibur_c46082_440, R2 = 4%), QSb.sdsu-4A.1 (SNP: IWA8475, R2 = 5.5%), QSb.sdsu-4B.1 (SNP: Excalibur_rep_c79414_306, R2 = 4%), QSb.sdsu-5A.1 (SNP: Kukri_rep_c104877_2166, R2 = 6%), and QSb.sdsu-7B.1 (SNP: TA005844-0160, R2 = 6%). Our study not only validates three (2D, 5A, and 7B) genomic regions identified in previous studies but also provides highly associated SNP markers for marker assisted selection. In addition, we identified three novel QTLs (QSb.sdsu-3A.1, QSb.sdsu-4A.1, and QSb.sdsu-4B.1) for SB resistance in wheat. Gene annotation analysis of the candidate regions identified nine NBS-LRR and 38 other plant defense-related protein families across multiple QTLs, and these could be used for fine mapping and further characterization of SB resistance in wheat. Comparative analysis with barley indicated the SB resistance locus on wheat chromosomes 2D, 3A, 5A, and 7B identified in our study are syntenic to the previously identified SB resistance locus on chromosomes 2H, 3H, 5H, and 7H in barley. The 10 highly resistant genotypes and SNP markers identified in our study could be very useful resources for breeding of SB resistance in wheat.
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Affiliation(s)
| | | | | | | | | | - Sunish K. Sehgal
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
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Ayana GT, Ali S, Sidhu JS, Gonzalez Hernandez JL, Turnipseed B, Sehgal SK. Genome-Wide Association Study for Spot Blotch Resistance in Hard Winter Wheat. FRONTIERS IN PLANT SCIENCE 2018. [PMID: 30034404 DOI: 10.3389/fpls00926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Spot blotch (SB) caused by Cochliobolus sativus (anamorph: Bipolaris sorokiniana) is an economically important disease of wheat worldwide. Under a severe epidemic condition, the disease can cause yield losses up to 70%. Previous approaches like bi-parental mapping for identifying SB resistant genes/QTLs exploited only a limited portion of the available genetic diversity with a lower capacity to detect polygenic traits, and had a lower marker density. In this study, we performed genome-wide association study (GWAS) for SB resistance in hard winter wheat association mapping panel (HWWAMP) of 294 genotypes. The HWWAMP was evaluated for response to B. sorokiniana (isolate SD40), and a range of reactions was observed with 10 resistant, 38 moderately resistant, 120 moderately resistant- moderately susceptible, 111 moderately susceptible, and 15 susceptible genotypes. GWAS using 15,590 high-quality SNPs and 294 genotypes we identified six QTLs (p = <0.001) on chromosomes 2D, 3A, 4A, 4B, 5A, and 7B that collectively explained 30% of the total variation for SB resistance. Highly associated SNPs were identified for all six QTLs, QSb.sdsu-2D.1 (SNP: Kukri_c31121_1460, R2 = 4%), QSb.sdsu-3A.1 (SNP: Excalibur_c46082_440, R2 = 4%), QSb.sdsu-4A.1 (SNP: IWA8475, R2 = 5.5%), QSb.sdsu-4B.1 (SNP: Excalibur_rep_c79414_306, R2 = 4%), QSb.sdsu-5A.1 (SNP: Kukri_rep_c104877_2166, R2 = 6%), and QSb.sdsu-7B.1 (SNP: TA005844-0160, R2 = 6%). Our study not only validates three (2D, 5A, and 7B) genomic regions identified in previous studies but also provides highly associated SNP markers for marker assisted selection. In addition, we identified three novel QTLs (QSb.sdsu-3A.1, QSb.sdsu-4A.1, and QSb.sdsu-4B.1) for SB resistance in wheat. Gene annotation analysis of the candidate regions identified nine NBS-LRR and 38 other plant defense-related protein families across multiple QTLs, and these could be used for fine mapping and further characterization of SB resistance in wheat. Comparative analysis with barley indicated the SB resistance locus on wheat chromosomes 2D, 3A, 5A, and 7B identified in our study are syntenic to the previously identified SB resistance locus on chromosomes 2H, 3H, 5H, and 7H in barley. The 10 highly resistant genotypes and SNP markers identified in our study could be very useful resources for breeding of SB resistance in wheat.
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Affiliation(s)
- Girma T Ayana
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Shaukat Ali
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Jagdeep S Sidhu
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Jose L Gonzalez Hernandez
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Brent Turnipseed
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Sunish K Sehgal
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
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Gurung S, Mahto BN, Gyawali S, Adhikari TB. Phenotypic and Molecular Diversity of Cochliobolus sativus Populations from Wheat. PLANT DISEASE 2013; 97:62-73. [PMID: 30722259 DOI: 10.1094/pdis-01-12-0092-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Spot blotch, caused by Cochliobolus sativus, is a devastating foliar disease of wheat in Nepal and in the Northern Great Plains of the United States. However, limited information on variation in virulence and genetic structure of C. sativus from wheat is available. In this study, pathogenic variation of 96 isolates of C. sativus from the Hill and Plain areas in Nepal (n = 48) and in the Central and Northern areas in North Dakota (n = 48) were evaluated on 12 differential wheat lines. DNA polymorphisms in all isolates were analyzed using eight selected amplified fragment length polymorphism primer combinations. Phenotypic data analysis showed the isolates varied greatly and were classified into 47 pathotypes. Cluster analysis indicated the isolates fell into three distinct groups with low, intermediate, and high virulence. Population genetic analysis revealed significant linkage disequilibrium ( = 0.066 to 0.292), indicating that sexual reproduction plays little or no role in evolution and disease epidemiology in wheat fields. Furthermore, the corrected standardized fixation index (G″ST = 0.05 and 0.02) showed no evidence of genetic differentiation in C. sativus populations. Collectively, these results confirmed high pathogenic and molecular diversity in the C. sativus populations collected from wheat foliar infections and will be useful to assist in developing resistant cultivars to manage this disease.
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Affiliation(s)
- Suraj Gurung
- Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, Salinas, CA 93905
| | - Baidya N Mahto
- Division of Plant Pathology, Nepal Agricultural Research Council, Khumaltar, Lalitpur, Nepal
| | - Sanjaya Gyawali
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada
| | - Tika B Adhikari
- Center for Integrated Pest Management and Department of Plant Pathology, North Carolina State University, 840 Main Campus Drive, Partners II Suite 1400, Centennial Campus, Raleigh 27606
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